The Rough Riders played their first season in 1994, fielding a team in the USISL that featured future US national team playerChris Armas, who would lead the team in scoring with eight goals and four assists. The team won the Northeast Division in its debut year, seven points ahead of North Jersey Dragons with a 13-5 record, and comfortably won through the first couple of rounds of the playoffs with victories over the New Jersey Imperials and the Dragons. The Rough Riders were placed in the "Raleigh Group" of the USISL 'Sizzling Nine' Championships, and qualified along with the Minnesota Thunder to face Greensboro Dynamo in the national semi final; they lost the game 2-1 in overtime, and Greensboro went on to take the title.

For their second season in 1995, the Rough Riders added several more players who would go on to excel in Major League Soccer, including national team goalkeeper Tony Meola, Jim Rooney, and Giovanni Savarese, who would be named the USISL regular season and playoff MVP, and who scored 23 goals during the campaign. The Rough Riders finished that season with a 19-1 record, top of the Coastal Conference for a second year running, and received a bye to the 'Sizzling Nine' Championship tournament. Wins over the Monterey Bay Jaguars and the New Mexico Chiles in group play took them to the national semi final for a second time. Unlike '95, the Rough Riders won their semi 5-2 over the Tampa Bay Cyclones, and then beat Minnesota Thunder 2-1 to win the USISL Championship.

The Rough Riders lost several players to the nascent MLS in 1996, including Meola and Savarese, but went on to have a successful season nevertheless, finishing with an 11-7 record and winning the North Atlantic Division. They beat Delaware Wizards 2-0 in the second round of the playoffs, and qualified from a 'Select Six' tournament group that comprised Minnesota Thunder and Hampton Roads Mariners, but lost 1-0 to the Richmond Kickers in the playoff semi-finals.

The Rough Riders finished 4th in the Northeast Division behind Rochester in 1998, and lost in the first round of the playoffs to the Richmond Kickers. 1999 was a similar story - 3rd behind the Rhinos in the regular season, and defeat in the first round of the playoffs to the Pittsburgh Riverdogs, although strikers John Wolyniec and Darko Kolic were much more prolific, scoring 15 and 7 goals respectively.

Fortunes improved significantly in 2000, as the Rough Riders took their first regular season title at this level, winning the Northeast Division by one point from the Rochester Raging Rhinos with a 16-9-4 record, with striker Edson Buddle contributing 11 of the team's 54 goals, and goalkeeper Paul Grafer posting a 1.29 GAA average. Their title came thanks to 9 bonus points earned for scoring 3 or more goals in a game. However, for a third straight season, playoff success eluded them, as they were dispatched 2-1 by the Toronto Lynx in the conference quarter finals.

The high of the first year of the new millennium was followed by a disappointing low in 2001 as the Rough Riders slumped to their first losing record in years - 8-16-4 - and finished sixth in the Northern Conference, a full 42 points behind divisional champions Hershey Wildcats, and out of the playoffs. Following this disastrous campaign, the team's ownership group decided to voluntarily relegate the team to the D3 Pro League for the 2002 campaign.

The Rough Riders bounced back magnificently in 2002; they won the D3-Pro League Atlantic Conference with an impressive 13-6-1 record, six points clear of New York Freedom in second place, with Derrick Etienne and Cordt Weinstein hitting 27 goals between them, and goalkeeper Billy Gatti maintaining an imposing presence between the pipes. They squeaked past New York on penalty kicks after a 2-2 tie in the playoff quarter finals, but enjoyed a dominant 3-0 win over the Connecticut Wolves in the semi final to reach the championship game at the first attempt; the final against Southern Conference champions Wilmington Hammerheads was a tight game, but the Rough Riders emerged as 2-1 victors, to take their second championship in franchise history.

The Rough Riders retained their divisional title in 2003, despite the league being re-aligned and renamed the Pro Select League, with a 13-4-3 record, 13 points clear of the New Jersey Stallions, their closest rival, and with Derrick Etienne again hitting 10 goals. The Rough Riders enjoyed some impressive victories in the regular season campaign, including a 3-0 victory on the road in May over Westchester Flames, a 4-1 road win over Jersey Falcons in early July, and a pair of comprehensive wins over Reading Rage, 5-1 and 4-1. The Rough Riders also made their second trip to the US Open Cup this year, but were upset in the second round by USL-PDL team Mid Michigan Bucks, who came from a goal down to register a 2-1 win. Despite being hot favorites to progress through the playoffs, they were upset by the Stallions 5-4 on penalties after a 0-0 tie in playoff regional final, and were left to reflect on a disappointing end to the season while the Wilmington Hammerheads went on to take the title.

The USL Pro Soccer League became the USL Second Division in 2005, and reverted to a single-table format, comprising just nine teams, all on the east coast. The season started in up-and-down fashion, with the Rough Riders never quite stringing a run of form together. An opening day 4-1 win over the Northern Virginia Royals was followed by a win over New Hampshire Phantoms, then 2 losses, then 2 wins, then three losses... and so it went. The team did enjoy a couple of comprehensive victories, during the mid-season, notably a second 4-1 win over Northern Virginia Royals in which Moussa Sy scored all four goals, and a 5-2 hammering of New Hampshire Phantoms in early July, but elsewhere things were tough; even their US Open Cup campaign ended early with a shocking 4-0 defeat to PDL side Ocean City Barons in the second round. The Rough Riders lost their final five games of the regular season, including a demoralizing 4-1 thrashing at home at the hands of Western Mass Pioneers, and finished the season in 6th place with a 7-13-0 record, missing the playoffs for a second straight year. Yet again, the prolific Derrick Etienne was Long Island's top scorer, with 9 goals, while Wilmer Cabrera contributed 5 assists.

2006 was arguably the worst season in the history of team, with them finishing the year at the bottom of the table with just three wins and fifteen goals to their credit. The season started in disastrous fashion with a shocking 13-game winless streak stretching from the opening day through to mid-July, and included several comprehensive losses: 5-0 to Richmond Kickers, 3-0 to Harrisburg City Islanders, 3-0 to Wilmington Hammerheads. Their first victory was against New Hampshire Phantoms at home, a scrappy 1-0 affair settled by an 84th minute strike from Moussa Sy; the high point of the season was the see-saw 3-2 win over Wilmington on the final day of the season, but it all too little too late for the Rough Riders. Following this disastrous campaign, the team chose to voluntarily relegate themselves to the USL-PDL for the 2007 season.

The Rough Riders first season in PDL actually began very promisingly, with four straight wins in their first four games, including a 3-1 win on the road over the Brooklyn Knights. Their excellent early-season form took them to the US Open Cup for the fourth time, but for the third time they suffered an early exit, although this time the result was less of a shock as it was at the hands of USL First Division stalwarts Rochester Raging Rhinos. Long Island's home form was their strong point, with five wins and a tie in front of their fans at Michael Tully Field; the highlight was the comprehensive 4-1 win over Vermont Voltage in mid-June. On the road, however, the Rough Riders were less dominant, their only further win coming in the final game of the season, 2-1 over the Westchester Flames. Elsewhere, they endured some difficult defeats, notably a 4-2 loss to the Rhode Island Stingrays in which the home team scored twice in the last 7 minutes. The Rough Riders' first season at level 4 ended with them fourth in the Northeast Division, 9 points behind divisional champs Cape Cod Crusaders, just out of the playoffs. Mike Grella was top scorer, with 5 goals, while Jose Batista contributed 5 assists.

Long Island were again playoff contenders in 2008. They tied their first game of the season 1-1 before demolishing Virginia Legacy 5-1 in the next fixture, with Mike Grella scoring a hat trick. The team was superb at home all season long, with five wins and three ties in their eight games at Michael Tully Field. They won an exiting encounter 4-3 over the Westchester Flames in early June, scored a 90th minute equalizer through goalkeeper Hasely Holder to tie 3-3 with Newark Ironbound Express, and flattened poor New Jersey Rangers 6-0, with Grella and Anthony Barberio both scoring 2 goals each. As was the case in 2007, their form on the road was their ultimate downfall, as the Rough Riders suffered four defeats, including a comprehensive 3-0 loss to the Ottawa Fury. Frustratingly, the Rough Riders finished the season third in the Northeast Division, just two points behind Newark Ironbound Express, and agonizingly out of the playoffs for the second straight year. Mike Grella and Michael Todd were top scorers, with 5 goals each, while both Todd and Tadeu Terra registered 4 assists.

This list of notable former players comprises players who went on to play professional soccer after playing for the team in the Premier Development League, or those who previously played professionally before joining the team.